Mercurial > repos > portiahollyoak > temp

comparison temp.xml @ 10:3200a0299230 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/portiahollyoak/Tools commit debe4684eaa00ffcae3c79e7581fdbe41da91d5d
author portiahollyoak
date Wed, 27 Apr 2016 11:44:13 -0400
parents 20a6e46295d6
children e19d9742c99b
comparison
equal deleted inserted replaced
9:20a6e46295d6 10:3200a0299230
1 <tool id ="run_TEMP" name="Run TEMP" version=" 0.1.1"> 1 <tool id ="run_TEMP" name="Run TEMP" version=" 0.1.2">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.1.19">samtools</requirement> 4 <!-- The following are classical toolshed packages and should be removed
5 once conda is deemed stable-->
6 <requirement type="package" version="1.6.922">bioperl</requirement>
7 <requirement type="package" version="0.7.12">bwa</requirement>
8 <requirement type="package" version="2.24">bedtools</requirement>
9 <!-- end of toolshed package definitions -->
5 <requirement type="package" version="1.6.924">perl-bioperl</requirement> 10 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
6 <requirement type="package" version="0.7.13">bwa</requirement> 11 <requirement type="package" version="0.7.13">bwa</requirement>
7 <requirement type="package" version="2.25.0">bedtools</requirement> 12 <requirement type="package" version="2.25.0">bedtools</requirement>
8 <requirement type="package" version="324">ucsc-twobittofa</requirement> 13 <requirement type="package" version="324">ucsc-twobittofa</requirement>
14 <requirement type="package" version="0.1.19">samtools</requirement>
9 </requirements> 15 </requirements>
10 <stdio> 16 <stdio>
11 <exit_code range="1:" /> 17 <exit_code range="1:" />
12 </stdio> 18 </stdio>
13 <command><![CDATA[ 19 <command><![CDATA[
14 20
15 ln -f -s "$alignment.metadata.bam_index" alignment.sorted.bam.bai && 21 ln -f -s "$alignment.metadata.bam_index" alignment.sorted.bam.bai &&
16 ln -f -s "$alignment" alignment.sorted.bam && 22 ln -f -s "$alignment" alignment.sorted.bam &&
17 bash $__tool_directory__/scripts/TEMP_Insertion.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} && ls -l && 23 bash $__tool_directory__/scripts/TEMP_Insertion.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} &&
18 bash $__tool_directory__/scripts/TEMP_Absence.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} && 24 bash $__tool_directory__/scripts/TEMP_Absence.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} &&
19 mv alignment.insertion.bp.bed $insertion_bed && 25 mv alignment.insertion.bp.bed $insertion_bed &&
20 mv alignment.insertion.refined.bp $insertion_bed_refined && 26 mv alignment.insertion.refined.bp $insertion_bed_refined &&
21 mv alignment.insertion.refined.bp.summary $insertion_summary && 27 mv alignment.insertion.refined.bp.summary $insertion_summary &&
22 mv alignment.absence.refined.bp.summary $absence_summary && 28 mv alignment.absence.refined.bp.summary $absence_summary &&